uint32_t parse_seq_str(const char *str, const char *file_name)
{
uint64_t k;
int64_t c;
uint32_t b;
if (scan_seq(str,&k,&b,&c))
{
check_and_set_base(b,file_name);
return get_seq(k,c);
}
return UINT32_MAX;
}
void test_scan_seq()
{
fprintf( stderr, " Running test_scan_seq ... " );
//char *seq = "AAAANTCGGCTNGGGG";
//char *seq = "AAAATCGGCTGGGG";
char *seq = "AAAAAAAAAAAAAAG";
size_t seq_len = strlen( seq );
size_t nmemb = 1 << 5;
uint *count_array = count_array_new( nmemb );
scan_seq( seq, seq_len, count_array );
// count_array_print( count_array, nmemb, 1 ); /* DEBUG */
fprintf( stderr, "done.\n" );
}
void scan_file( char *file, seq_entry *entry, uint *count_array )
{
/* Martin A. Hansen, September 2008 */
/* Scan all FASTA entries of a file. */
FILE *fp = read_open( file );
while ( fasta_get_entry( fp, &entry ) == TRUE )
{
fprintf( stderr, " Scanning: %s (%zu nt) ... ", entry->seq_name, entry->seq_len );
scan_seq( entry->seq, entry->seq_len, count_array );
fprintf( stderr, "done.\n" );
}
close_stream( fp );
}